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alfred-workflows

:metal: A collection of Alfred 3 and 4 workflows that will rock your world

awesome-obsidian

🕶️ Awesome stuff for Obsidian

bin

scripts

bio_tools

Useful bioinformatic scripts

biocode

Bioinformatics code libraries and scripts

cafe_fig

A tool to extract and visualize the results of CAFE (Computational Analysis of gene Family Evolution)

cancertocellline

R codes for the nature communications paper "Evaluating cell lines as models for metastatic breast cancer through integrative analysis of genomic data""

causal_salad_2021

One day course on causal inference, MPI-EVA 9 September 2021

genome_analysis

gffutils

GFF and GTF file manipulation and interconversion

gffutils-1

Convert, explore, and manipulate GFF and GTF files (used in bioinformatics) using a sqlite-based approach

intro-to-rnaseq-hpc-salmon-flipped

Introduction to bulk RNA-seq

jaltgenome

Raw scripts for de novo assembling a Jaltomata genome. Publication: Wu, M., Kostyun, J. and Moyle, L., 2018. Genome sequence of Jaltomata addresses rapid reproductive trait evolution and enhances comparative genomics in the hyper-diverse Solanaceae. Genome Biology and Evolution, evy274.

jcvi

Python library to facilitate genome assembly, annotation and comparative genomics

kaks_error_bars

A simple script and example data file to draw barplots of multiple protein's pairwise dN/dS values, with error bars!

learning_vcf_file

Learning the Variant Call Format

mcmctree_tree_prep

making input tree for mcmctree

pbbioconda

PacBio Secondary Analysis Tools on Bioconda

quota-alignment

Guided synteny alignment between duplicated genomes (within specified quota constraint)

research_pipline

rgaat

Reference based genome assembly and annotation tool for new genome and known genome upgrade

snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data

tama

Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)

whole-genome-reseq

Scripts for the analysis of low-coverage whole genome resequencing data